Variant report

Variant	rs12927256
Chromosome Location	chr16:12057883-12057884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:12057501-12061734	GM18505	blood:	n/a	n/a
2	ZNF384	chr16:12057715-12058728	K562	blood:	n/a	n/a
3	POLR2A	chr16:12057110-12063123	GM12891	blood:	n/a	n/a
4	MTA3	chr16:12057615-12059791	GM12878	blood:	n/a	n/a
5	MXI1	chr16:12057829-12059429	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:12057323-12060663	GM12878	blood:	n/a	n/a
7	ZNF384	chr16:12057764-12058459	GM12878	blood:	n/a	n/a
8	PML	chr16:12057873-12059573	GM12878	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12008413..12010461-chr16:12056035..12059014,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-166B2.1.1-2	chr16:12057748-12057883	NONHSAT140610

No data

Variant related genes	Relation type
TNFRSF17	TF binding region
ENSG00000103342	Chromatin interaction
ENSG00000266163	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10451099	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10468251	0.84[ASN][1000 genomes]
rs10852345	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10852346	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11075035	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11075036	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075037	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11570137	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11570173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11864397	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12597378	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12926535	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12928141	0.86[ASN][1000 genomes]
rs12929036	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12929544	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12929852	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12933691	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12934607	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2017662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs365423	0.82[ASN][1000 genomes]
rs366262	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3743591	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851002	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851003	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs387871	0.84[ASN][1000 genomes]
rs3916675	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57171695	0.88[ASN][1000 genomes]
rs58398910	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59320000	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6498255	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6498256	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6498257	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7189024	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7190636	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7191310	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7195514	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72782778	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8046211	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8047277	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051343	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8055129	0.87[ASN][1000 genomes]
rs8060611	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8062121	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9922422	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9922795	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv571459	chr16:12046899-12062396	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12040400-12065400	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12042200-12064400	Weak transcription	Fetal Stomach	stomach
3	chr16:12048600-12064800	Weak transcription	Thymus	Thymus
4	chr16:12050400-12058200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:12052200-12067600	Weak transcription	Osteobl	bone
6	chr16:12052200-12069600	Weak transcription	Primary T cells from cord blood	blood
7	chr16:12052400-12058600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:12052400-12066800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:12053000-12058600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr16:12053000-12065800	Weak transcription	Placenta	Placenta
11	chr16:12053200-12058600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:12053400-12058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12053400-12058800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:12054600-12069400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr16:12055000-12059000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:12055800-12058600	Enhancers	Primary B cells from cord blood	blood
17	chr16:12056200-12058600	Enhancers	Primary B cells from peripheral blood	blood
18	chr16:12056600-12058200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:12056800-12069400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr16:12057000-12060000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr16:12057200-12058200	Flanking Active TSS	GM12878-XiMat	blood
24	chr16:12057400-12058000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr16:12057400-12059400	Enhancers	K562	blood
26	chr16:12057600-12059800	Enhancers	Fetal Thymus	thymus
27	chr16:12057800-12058800	Weak transcription	NHEK	skin

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